Software for Structural Bioinformatics of Nucleic Acid

核酸结构生物信息学软件

• 批准号: 7342843
• 负责人: John SantaLucia
• 金额: $ 24.12万
• 依托单位: WAYNE STATE UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2005
• 资助国家: 美国
• 起止时间: 2005-02-01 至 2009-01-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7342843
• 关键词: Algorithms; Amber; Antibiotics; Base Pairing; Base Sequence; Bioinformatics; Biological; Charge; Chemicals; Classification; Communities; Computer software; DNA; DNA Sequence; DNA Structure; Databases; Development; Escherichia; Functional RNA; Genbank; Goals; Growth; Homology Modeling; Link; Methodology; Methods; Modification; Molecular Structure; Nucleic Acids; Nucleotides; Property; Protein Biosynthesis; Proteins; Publishing; RNA; RNA Folding; Ribosomes; Secondary to; Sequence Alignment; Solutions; Structural Biologist; Structural Models; Structure; Testing; Thermodynamics; Validation; Work; Writing; X-Ray Crystallography; blind; genome sequencing; insertion/deletion mutation; molecular dynamics; molecular mechanics; novel; programs; quantum; restraint; simulation; three dimensional structure; tool; trend

DESCRIPTION (provided by applicant): Methods for macromolecular structure determination cannot keep pace with the exponential growth of biological sequence databases. The goal of this proposal is to develop a new software platform for structural bioinformatics of nucleic acids that will allow analysis of existing structures and accurate prediction of 3D structures. This will be achieved in four specific aims: Aim 1: Write software for homology modeling of nucleic acids. Software will be written to "thread" a sequence whose 3D structure is unknown into a known template structure. This methodology will leverage genome sequencing projects by allowing the automated 3D structure prediction of many functional RNAs. Aim 2: Write software for de novo 3D structure prediction of nucleic acids. Secondary structures from a dynamic programming algorithm will be converted into rough 3D structures using a novel BUILDER algorithm that utilizes a motif database. Classical molecular dynamics simulations will be used to refine the structures. The result will be accurate de novo 3D structure predictions of RNA and DNA. Aim 3: Develop an extended forcefield and optimization algorithms for nucleic acids. The AMBER forcefield will be extended to include parameters for the >100 modified nucleotides that occur in natural RNAs. The forcefields will also be extended to include pseudo-potential terms for gap penalties, solution trends in DNA and RNA folding thermodynamics, and experimental restraints. This modified forcefield will be used to rank predicted 3D structures. New geometry optimization algorithms will also be developed. Aim 4: A systematic validation of the quality of predictions of the software produced by Aims 1,2 and 3 will be performed. The software will be used to predict all the published 3D structures determined by X-ray crystallography or NMR. A blind test will be performed by inviting structural biologists to submit unpublished structures for prediction by our algorithms (similar to CASP for proteins).

描述(由申请人提供)： 大分子结构的测定方法跟不上生物序列数据库的指数增长。这项提议的目标是开发一个新的核酸结构生物信息学软件平台，使其能够分析现有结构和准确预测三维结构。这将通过四个具体目标来实现： 目标1：编写核酸同源模型软件。将编写软件来将其3D结构未知的序列“串”到已知的模板结构中。这种方法将通过允许自动预测许多功能RNA的3D结构来利用基因组测序项目。 目的2：编写核酸从头三维结构预测软件。来自动态规划算法的二级结构将使用一种利用Motif数据库的新型构建器算法转换为粗略的3D结构。经典的分子动力学模拟将被用来改进结构。其结果将是对RNA和DNA的准确从头3D结构预测。 目的3：发展核酸的扩展力场和优化算法。琥珀力场将扩展到包括天然RNA中出现的&gt；100修饰核苷酸的参数。力场还将扩展到包括间隙惩罚的伪势项、DNA和RNA折叠热力学中的溶液趋势以及实验限制。该修改后的力场将用于对预测的3D结构进行排序。还将开发新的几何优化算法。 目标4：将对目标1、2和3制作的软件的预测质量进行系统验证。该软件将用于预测所有由X射线结晶学或核磁共振确定的已发表的3D结构。盲法测试将通过邀请结构生物学家提交未发表的结构，以供我们的算法预测(类似于蛋白质的CASP)。